I'm not so sure what you're describing, but it sounds like you have wooden sash (window frames) with individual thermopane lites (window panes). This would be pretty unusual but not unheard of. I have never seen thermopanes installed with glazing compound and I'd guess you do have lites installed with wooden stops as you described. I'd suggest scraping the paint back from one to see what you're dealing with and maybe trying to pry the stops up gently to see how hard it is. You might also call some glass shops to price the replacement panes. If you have a lot of failed thermopanes it might cost more than it's worth to replace just the lites. Windows could be cheaper especially if you consider the labor involved. Call more than one glass shop, as prices can vary a lot.
I have replaced thermopanes successfully but always in metal sashes. One thing I've learned is to find out from the supplier what sealants are compatable with the new thermopane windows. It can vary from manufacturer to manufacturer and the wrong sealant can cause the thermopane to fail again.